Another example using 1920 super resolution for Sega Genesis. In this case, i used 1920 for match refresh_rate with modeline, and i reserved 2560 for 60hz.
Another tip is split config files for system: retroarch.exe -L %fullpath%cores\genesis_plus_gx_libretro.dll --config %fullpath%config\retroarchcustom.cfg --appendconfig %fullpath%config\genesis.cfg %1
crt_switch_resolution_super = "1920"
video_aspect_ratio = "8.000000"
video_refresh_rate = "59.922745"
video_rotation = "0"
video_scale = "1.000000"
video_scale_integer = "false"
video_smooth = "false"
video_crop_overscan = "false"
video_threaded = "false"
aspect_ratio_index = "23"
custom_viewport_height = "224"
custom_viewport_width = "1920"
custom_viewport_x = "0"
custom_viewport_y = "0"